Sai Pooja wrote:
Hi,
I am getting these notes when I run grompp:
NOTE 3 [file Init/ffsb_init.top]:
The largest charge group contains 12 atoms.
Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
initialising group options...
processing index file...
Analysing residue names:
There are: 3484 OTHER residues
There are: 67 PROTEIN residues
There are: 0 DNA residues
There are: 0 RNA residues
Analysing Protein...
Analysing Other...
Making dummy/rest group for Acceleration containing 11343 elements
Making dummy/rest group for Freeze containing 11343 elements
Making dummy/rest group for VCM containing 11343 elements
Number of degrees of freedom in T-Coupling group Protein is 1777.76
Number of degrees of freedom in T-Coupling group non-Protein is 20898.23
Making dummy/rest group for User1 containing 11343 elements
Making dummy/rest group for User2 containing 11343 elements
Making dummy/rest group for XTC containing 10450 elements
Making dummy/rest group for Or. Res. Fit containing 11343 elements
Making dummy/rest group for QMMM containing 11343 elements
T-Coupling has 2 element(s): Protein non-Protein
Energy Mon. has 2 element(s): Protein non-Protein
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 2 element(s): Protein rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
Largest charge group radii for Van der Waals: 0.288, 0.263 nm
Largest charge group radii for Coulomb: 0.288, 0.263 nm
NOTE 4 [file nvtp.mdp]:
The sum of the two largest charge group radii (0.551009) is larger than
rlist (2.000000) - rvdw (2.000000)
Can someone tell me how to correct these?
Note 3 is explained in detail in the error message. Beyond that, read about the
group concept in the manual.
I've never seen Note 4 before, but a 2-nm cutoff is a bit strange for a protein
simulation. Any reason you're using such large cutoffs? You may also want to
provide your whole .mdp file to see if anyone can spot the underlying issue.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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